Section I. Introduction 1. Book introduction 2. MS Proteomic Overview

Section II. Sample Preparation 3. Sample preparation from mammalian cell lines 4. Sample preparation for proteomics and MS from clinical tissue 5. Sample preparation for proteomics and MS from biological fluids, e.g. serum/plasma from patient blood 6. Sample preparation for proteomics and MS from bacterial and fungal samples 7. Sample preparation for proteomics and MS from urine samples including exosome isolation 8. Sample preparation for proteomics and MS from animal samples 9. Subcellular fractionation methods for proteomic analysis

Section III. Protein Digestion 10. In gel digestion for mass spectrometry 11. In solution digestion for mass spectrometry

Section IV. MS Proteomic Analysis Protocols 12. Protocols for Label-free LC-MS/MS proteomic analysis 13. Protocols for TMT labelled LC-MS/MS analysis 14. Phosphorylation enrichment for phosphoproteomic analysis 15. Ubiquitination enrichment for ubiquitinome PTM analysis 16. Glycosylation enrichment and analysis 17. LC-MS for protein identification and PTM analysis (e.g. methylation)